BiKEGG by using a combination of manual verification and computational methods takes a genome-scale metaboli model (GEM) as input and scrutinizes the KEGG REACTION database to find all reactions equivalent to those in the input model. Currently, the corresponding KEGG reactions for 79 BiGG models have been generated with this approach.
All shared reactions among all 79 GEMs on BiGG were stored as a separate .mat file (namely UniModel). UniModel can be further used to find corresponding reactions in BiGG based on the genome annotation of an organism of interest in the KEGG (using Precons tool), which may be particularly beneficial for initial pre-draft reconstruction process.
Classical KEGG pathways | Customized metabolic maps
BiKEGG takes a flux distributions and a set of BiGG reaction IDs corresponding to the flux data (from COBRA toolbox) as input, and retrieve the set of equivalent KEGG reactions based on the previously generated KEGG reaction correspondences (e.g. UniModel). The user can then choose the set of KEGG pathways to be visualized. Finally, a set of equivalent KEGG reactions for the input BiGG model, the set flux data corresponding to this set of reactions and a number of users’ selected KEGG maps are generated. BiKEGG’s approach for visualization falls into two categories: 1- it can overlay the numerical results on the classical KEGG pathways; and 2- can generate customized metabolic maps based on KEGG global metabolic pathway. These customized metabolic maps contain reaction directionality based on BiGG models, which allow for a better understating and analysis of the visualized in silico results. Furthermore, BiKEGG is capable of visualizing the reaction fluxes for one or two different static conditions, and for dynamic conditions in an animated manner.
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